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<h1>
<a href="index.html">AQUA</a></h1>

<address>
Jurgen Doreleijers, Madison, <a href="mailto:jurgenfd@gmail.com">jurgenfd@gmail.com</a></address>

<address>
Ton Rullmann, Utrecht</address>

<br>&nbsp;</td>

<td>
<blockquote>
<div align=right><img SRC="aqua.gif" height=108 width=108 align=RIGHT></div>
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<h2>

<hr WIDTH="100%"></h2>

<h2>
README</h2>

<h2>
Contents</h2>

<ol>
<li>
<a href="#1. ACKNOWLEDGEMENTS">ACKNOWLEDGMENTS</a></li>

<li>
<a href="#2. SCOPE OF PROGRAMS">SCOPE OF PROGRAMS</a></li>

<li>
<a href="#3. INSTALLING AQUA">INSTALLING AQUA</a></li>

<li>
<a href="#4. USING AQUA">USING AQUA</a></li>
</ol>

<p><br>
<hr WIDTH="100%">
<h2>
<a NAME="1. ACKNOWLEDGEMENTS"></a>1. Acknowledgments</h2>
Software contributions by the following people are acknowledged:
<ul>
<li>
Kris Boulez, Biomolecular NMR unit, University of Ghent: qanal script [analysis
of aqpc output]</li>

<li>
Roman Laskowski, Biomolecular Structure and Modelling Group, University
College, London: Range.c code [processing of file with residue/model selection
info], getproj.c code [file name processing]</li>

<li>
Mia Raves, NMR spectroscopy Utrecht: Debugging the script 'aq2xplor-tors'
for converting Aqua formatted torsion angle restraint files to XPLOR format
.</li>

<li>
Gert Vriend, EMBL Heidelberg: Proton nomenclature check in WHATIF</li>

<li>
Greg Warren, Dept. of Molecular Biophysics and Biochemistry, Yale University:
New version of convXPLORdistrestr script [conversion XPLOR restraints]</li>
</ul>
We also thank all of you who contributed by reporting problems and asking
questions. It really helped to improve the programs!
<p>
<hr WIDTH="100%">
<h2>
<a NAME="2. SCOPE OF PROGRAMS"></a>2. Scope of the programs</h2>
The Aqua program suite in this distribution calculates restraint violations
from:
<ul>
<li>
&nbsp;&nbsp;&nbsp; a PDB or BIOSYM file containing one or more coordinate
sets</li>

<li>
&nbsp;&nbsp;&nbsp; distance restraint file(s) in Aqua format</li>
</ul>
Conversion scripts are available to convert DISGEO, XPLOR, BIOSYM and DISMAN/DIANA
restraint files to Aqua format. These scripts can also generate torsion
angle restraint files, which are read by Procheck-NMR. User-defined conversion
scripts can easily be linked into the master script.
<p>Conversion from Aqua to XPLOR, BIOSYM, DIANA and NMR-STAR format is
now also available.
<p>Both "MR" and "non-MR" restraint files can be handled (MR is used here
to indicate the restraint file structure currently employed by the PDB;
the name was taken from the file name extension assigned by the PDB).
<p>Coordinates of pseudo-atoms are generated when necessary. Presently
this is done by calculating the geometric average of the corresponding
proton positions.
<p>The output files contain a full listing of:
<ul>
<li>
Distances in all models</li>

<li>
Violations in all models</li>

<li>
Completeness and redundancy of the NOEs</li>

<li>
Summaries:</li>

<ul>
<li>
per model;</li>

<li>
per restraint;</li>

<li>
per residue (calculated over all models and for each individual model)</li>

<li>
per range-type (sequential, medium, long etc.)</li>
</ul>

<li>
These summaries list:</li>

<ul>
<li>
number of violated restraints;</li>

<li>
largest violation;</li>

<li>
total violation; for each of three groups of restraints: upper bound violations,
lower bound violations, "big" violations.</li>
</ul>

<li>
Number of restraints for each residue</li>

<li>
Number of restraints for each range-type (sequential, medium, long etc.)</li>
</ul>
Facilities are available:
<ul>
<li>
For extracting data from these files on a keyword basis</li>

<li>
For producing more condensed summaries (containing average and r.m.s.d.
violation values; number of (violated) restraints; sorted lists of first
"N" largest violations) per model and overall.</li>

<li>
For restricting the analysis to a subset of residues and/or models.</li>

<li>
For sorting restraints and violation lists.</li>

<li>
For selecting residue ranges from PDB files and from restraint files.</li>
</ul>
The violations and numbers of restraints can also be visualized with Procheck-NMR.
<p>New modules allow:
<ul>
<li>
Checking and correcting the consistency of stereospecific assignments.</li>

<li>
Checking the redundancy and completeness of NOE distance restraints.</li>

<li>
Correcting the nomenclature of restraints and coordinates simultaneously,
to comply with IUPAC definitions.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="3. INSTALLING AQUA"></a>3. Installing AQUA</h2>
1. Uncompress and unpack the archive (substituting X.Y for the version
you downloaded):
<pre>&nbsp;&nbsp;&nbsp; tar -zxvf aquaX.Y.tar.gz</pre>
This will create a subdirectory called 'aquaX.Y' in the present working
directory. If the z option doesn't work on your system you'll have to use
gunzip or uncompress before the tar command.
<p>2. Follow the instructions in the file <a href="HOW_TO_INSTALL.html">HOW_TO_INSTALL</a>.
<p>
<hr WIDTH="100%">
<h2>
<a NAME="4. USING AQUA"></a>4. Using AQUA</h2>
Please see the file <a href="HOW_TO_USE.html">HOW_TO_USE</a>. After installing
and initializing the 'qhelp' command gives easy access to the documentation.
<p>
<hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a> or <a href="mailto:webmaster@bmrb.wisc.edu">webmaster</a>
for help, when required.
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